Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes

Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered molecular dynamics to assess the strength of protein-peptide interactions. The idea behind using steered molecular dynamics simulations is that the mechanical stability can be used as a promising and an efficient alternative to computationally highly demanding estimation of binding affinity. However, mechanical stability defined as a peak in force-extension profile depends on the choice of the pulling direction. Here we propose an uncommon choice of the pulling direction along resultant dipole moment vector, which has not been explored in simulations so far. Using explicit solvent all-atom MD simulations, we apply steered molecular dynamics technique to probe mechanical resistance of protein-peptide system pulled along two different vectors. A novel pulling direction, along the resultant dipole moment vector, results in stronger forces compared to commonly used peptide unbinding along center of masses vector. Our results demonstrate that resultant dipole moment is one of the factors influencing the mechanical stability of protein-peptide complex.Comment: 11 pages, 4 figures, 2 table

Steered Molecular Dynamics Simulations of NAD Unbinding from GAPDH and LDH

Protein-ligand interactions play an important role in understanding biophysical processes including the glycolytic pathway. Calculation of the energy profile of ligand unbinding is essential for understanding possible substrate channeling of nicotinamide adenine dinucleotide (NAD) between lactate dehydrogenase (LDH) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Herein, steered molecular dynamics (SMD) simulations elucidate the process of NAD unbinding from LDH and GAPDH. Brownian dynamics (BD) simulate, using the energy reaction criterion, NAD diffusion towards the binding site of GAPDH or LDH to identify potential residues where strong protein-ligand coulombic interactions exist. These residues are used to design several dissociation pathways for the SMD simulations. Simulations either apply a harmonic guiding potential or a constant force SMD to perform center of mass (COM) pulling of the NAD. The two ligands in the tetrameric GAPDH protein are successfully released from the binding pocket using a force constant k ≥ 5000 kJ/mol/nm2 or a constant force F ≥ 600 pN, within the first 4.2 ns of simulation time. A constant force of 600 pN is enough to pull out three of the four ligands from their corresponding LDH binding sites within the first 0.5 to 1.2 ns of simulation time. Upon releasing the ligand from the binding site, NAD conformational changes are traced, starting with a stretched, open conformation in the binding site and ending with a bent structure in solution. The bent structure is consistent with previous experimental and simulation data of NAD free in solution. The unbinding free energies associated with the NAD release along the proposed pathways are calculated using the Jarzynski equality, in the stiff-spring approximation of pulling

AFM Force Spectroscopy and Steered Molecular Dynamics Simulation of Protein Contactin 4

We use a single molecule atomic force spectroscopy combined with the steered molecular dynamics simulation to determine a mechanical behavior of neural cell adhesion protein contactin during its unfolding. Force curves typical for modular proteins were observed, showing at most four unfolding peaks. The analysis of force spectra performed within worm-like chain model of polymer elasticity showed the presence of three unfolding lengths. Small plateaus, most likely resulting from forced transitions within domains were observed for the first time. Steered molecular dynamics simulations help to determine atomistic picture of domain unfolding

Steered Molecular Dynamics Simulations of NAD Unbinding from GAPDH and LDH

Protein-ligand interactions play an important role in understanding biophysical processes including the glycolytic pathway. Calculation of the energy profile of ligand unbinding is essential for understanding possible substrate channeling of nicotinamide adenine dinucleotide (NAD) between lactate dehydrogenase (LDH) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Herein, steered molecular dynamics (SMD) simulations elucidate the process of NAD unbinding from LDH and GAPDH. Brownian dynamics (BD) simulate, using the energy reaction criterion, NAD diffusion towards the binding site of GAPDH or LDH to identify potential residues where strong protein-ligand coulombic interactions exist. These residues are used to design several dissociation pathways for the SMD simulations. Simulations either apply a harmonic guiding potential or a constant force SMD to perform center of mass (COM) pulling of the NAD. The two ligands in the tetrameric GAPDH protein are successfully released from the binding pocket using a force constant k ≥ 5000 kJ/mol/nm2 or a constant force F ≥ 600 pN, within the first 4.2 ns of simulation time. A constant force of 600 pN is enough to pull out three of the four ligands from their corresponding LDH binding sites within the first 0.5 to 1.2 ns of simulation time. Upon releasing the ligand from the binding site, NAD conformational changes are traced, starting with a stretched, open conformation in the binding site and ending with a bent structure in solution. The bent structure is consistent with previous experimental and simulation data of NAD free in solution. The unbinding free energies associated with the NAD release along the proposed pathways are calculated using the Jarzynski equality, in the stiff-spring approximation of pulling

Influence of subunit structure on the oligomerization state of light harvesting complexes: a free energy calculation study

Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine identical subunits, respectively. Here, we investigate computationally what factors govern the different ring sizes. Starting from the crystal structure geometries, we embed two subunits of each species into their native lipid-bilayer/water environment. Using molecular dynamics simulations with umbrella sampling and steered molecular dynamics, we probe the free energy profiles along two reaction coordinates, the angle and the distance between two subunits. We find that two subunits prefer to arrange at distinctly different angles, depending on the species, at about 42.5 deg for Rs. molischianum and at about 38.5 deg for Rps. acidophila, which is likely to be an important factor contributing to the assembly into different ring sizes. Our calculations suggest a key role of surface contacts within the transmembrane domain in constraining these angles, whereas the strongest interactions stabilizing the subunit dimers are found in the C-, and to a lesser extent, N-terminal domains. The presented computational approach provides a promising starting point to investigate the factors contributing to the assembly of protein complexes, in particular if combined with modeling of genetic variants.Comment: 28 pages, 7 figures, LaTeX2e - requires elsart.cls (included), submitted to Chemical Physic